Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_106719055.1 CU100_RS23405 homoserine O-acetyltransferase
Query= SwissProt::Q9AAS1 (382 letters) >NCBI__GCF_003010935.1:WP_106719055.1 Length = 395 Score = 524 bits (1349), Expect = e-153 Identities = 247/367 (67%), Positives = 302/367 (82%), Gaps = 2/367 (0%) Query: 17 FPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGW 76 F A++PL LDSG + IAYQ YG+LNADKSNA+L+CHALTGDQHVA+ HP TGKPGW Sbjct: 28 FGADKPLHLDSGVSLSPFRIAYQAYGELNADKSNAILVCHALTGDQHVANVHPVTGKPGW 87 Query: 77 WQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQ 136 W+ L+GPGKP+D R+F+ICSNV+GGC+GSTGPASINP TGK Y L P+ITIADMVRAQ Sbjct: 88 WELLIGPGKPIDTDRYFVICSNVLGGCLGSTGPASINPETGKPYALDLPIITIADMVRAQ 147 Query: 137 AMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGR 196 AMLV G+E LFAV+GGSMGGMQV +WA + +++F+AV +A+ +RHS+QNIAFHEVGR Sbjct: 148 AMLVEHFGIEQLFAVIGGSMGGMQVLEWASSHSDKVFAAVAIATGARHSSQNIAFHEVGR 207 Query: 197 QAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGF 255 QA+MADP+W+ G Y E G P KGL+VARMAAHITYLSE AL KFGR LQ R +++GF Sbjct: 208 QAVMADPEWKEGRYLEAGTVPRKGLSVARMAAHITYLSETALHNKFGRNLQDRQNVTFGF 267 Query: 256 DADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCV 315 DADFQ+ESYLRHQG++FV+RFD NSYLY+TRAMDYFD+AA HGG LA AF ++ RFC+ Sbjct: 268 DADFQIESYLRHQGTTFVERFDPNSYLYMTRAMDYFDLAAEHGGRLADAFAGSK-TRFCI 326 Query: 316 LSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLASA 375 +SF+SDWL+PT+E+R + AL AAGA +F EIESD+GHD+FLLDEP M + + GF+ SA Sbjct: 327 VSFTSDWLFPTSESRMVAHALNAAGASVSFVEIESDRGHDSFLLDEPEMFSTITGFIRSA 386 Query: 376 ERDRGLV 382 R RGLV Sbjct: 387 ARARGLV 393 Lambda K H 0.321 0.135 0.417 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 521 Number of extensions: 18 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 382 Length of database: 395 Length adjustment: 30 Effective length of query: 352 Effective length of database: 365 Effective search space: 128480 Effective search space used: 128480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 bits)
Align candidate WP_106719055.1 CU100_RS23405 (homoserine O-acetyltransferase)
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01392.hmm # target sequence database: /tmp/gapView.1200511.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01392 [M=351] Accession: TIGR01392 Description: homoserO_Ac_trn: homoserine O-acetyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-148 479.6 0.0 3.2e-148 479.4 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106719055.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106719055.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.4 0.0 3.2e-148 3.2e-148 2 350 .. 31 383 .. 30 384 .. 0.98 Alignments for each domain: == domain 1 score: 479.4 bits; conditional E-value: 3.2e-148 TIGR01392 2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsry 73 +++l+l+sG ls +++ay+ yG+lna+++Na+lvcHaltg++hva+ + + k GWW+ l+Gpg+++dt+ry NCBI__GCF_003010935.1:WP_106719055.1 31 DKPLHLDSGVSLSPFRIAYQAYGELNADKSNAILVCHALTGDQHVANVHPVTGKpGWWELLIGPGKPIDTDRY 103 589********************************************99977767****************** PP TIGR01392 74 fvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewa 146 fv+c+NvlG+c GstgP+sinpetgkpy ++P +ti D+v+aq++l++++g+e+l+av+GgS+GGmq+lewa NCBI__GCF_003010935.1:WP_106719055.1 104 FVICSNVLGGCLGSTGPASINPETGKPYALDLPIITIADMVRAQAMLVEHFGIEQLFAVIGGSMGGMQVLEWA 176 ************************************************************************* PP TIGR01392 147 lsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARmlalltYrseesl 218 s ++v ++v++at+ar+s+q+iaf+ev rqa+++Dpe+++G+y e + P+kGL++ARm a++tY+se++l NCBI__GCF_003010935.1:WP_106719055.1 177 SSHSDKVFAAVAIATGARHSSQNIAFHEVGRQAVMADPEWKEGRYLEAGtVPRKGLSVARMAAHITYLSETAL 249 ***********************************************999*********************** PP TIGR01392 219 eerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkika 291 +++fgr+ ++++++++ ++++f++esylr+qg++fverFd nsYl++t+a+d++dla+++ ++l++a++ k+ NCBI__GCF_003010935.1:WP_106719055.1 250 HNKFGRNLQDRQNVTFGFDADFQIESYLRHQGTTFVERFDPNSYLYMTRAMDYFDLAAEHGGRLADAFAGSKT 322 ************************************************************************* PP TIGR01392 292 pvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350 ++++v+++sD+lf+++e++ +a+al+aa+++ ++eies++GHD+Fll++ ++ ++i+ f+ NCBI__GCF_003010935.1:WP_106719055.1 323 RFCIVSFTSDWLFPTSESRMVAHALNAAGASvsFVEIESDRGHDSFLLDEPEMFSTITGFI 383 ****************************99999**********************999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (395 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 19.71 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory